Nextflow workflow report

[cranky_curie]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM (SRR11452476)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM (SRR11452476)` terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

  samtools \
      merge \
      --threads 1 \
       \
      --reference human_g1k_v37_decoy.fasta \
      SRR11452476.recal.cram \
      1/SRR11452476_GL000222.recal.cram 2/SRR11452476_18_1-78077248.recal.cram 3/SRR11452476_GL000200.recal.cram 4/SRR11452476_GL000193.recal.cram 5/SRR11452476_6_1-171115067.recal.cram 6/SRR11452476_15_1-102531392.recal.cram 7/SRR11452476_22_1-51304566.recal.cram 8/SRR11452476_GL000225.recal.cram 9/SRR11452476_9_1-141213431.recal.cram 10/SRR11452476_21_1-48129895.recal.cram 11/SRR11452476_14_1-107349540.recal.cram 12/SRR11452476_X_1-155270560.recal.cram 13/SRR11452476_Y_1-59373566.recal.cram 14/SRR11452476_GL000192.recal.cram 15/SRR11452476_hs37d5_1-35477943.recal.cram 16/SRR11452476_GL000194.recal.cram 17/SRR11452476_GL000212.recal.cram 18/SRR11452476_GL000215.recal.cram 19/SRR11452476_GL000216.recal.cram 20/SRR11452476_GL000219.recal.cram 21/SRR11452476_GL000205.recal.cram 22/SRR11452476_GL000224.recal.cram 23/SRR11452476_NC_007605_1-171823.recal.cram 24/SRR11452476_GL000195.recal.cram 25/SRR11452476_GL000217.recal.cram 26/SRR11452476_13_1-115169878.recal.cram 27/SRR11452476_GL000223.recal.cram 28/SRR11452476_GL000199.recal.cram 29/SRR11452476_16_1-90354753.recal.cram 30/SRR11452476_17_1-81195210.recal.cram 31/SRR11452476_2_1-243199373.recal.cram 32/SRR11452476_8_1-146364022.recal.cram 33/SRR11452476_4_1-191154276.recal.cram 34/SRR11452476_3_1-198022430.recal.cram 35/SRR11452476_11_1-135006516.recal.cram 36/SRR11452476_10_1-135534747.recal.cram 37/SRR11452476_7_1-159138663.recal.cram 38/SRR11452476_20_1-63025520.recal.cram 39/SRR11452476_12_1-133851895.recal.cram 40/SRR11452476_5_1-180915260.recal.cram 41/SRR11452476_19_1-59128983.recal.cram 42/SRR11452476_1_1-249250621.recal.cram
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Command wrapper:
  ls: SRR11452476.recal.bam: No such file or directory
  ls: *.csi: No such file or directory

Work dir:
  /input/data/work/dc/728b91c307e04b744144b3944601df

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
18-Nov-2023 20:30:25 - 19-Nov-2023 00:56:35 (duration: 4h 26m 10s)
  3935 succeeded  
  0 cached  
  0 ignored  
  1 failed  
Nextflow command
nextflow run /input/sarek -profile test_full -c /experiments/experiment/sarek/nextflow.config -c /experiments/experiment/nextflow_cws.config -c /experiments/experiment/nextflow_nfs.config
CPU-Hours
882.6 (0.1% failed)
Launch directory
/experiments/experiment/launch
Work directory
/input/data/work
Project directory
/input/sarek
Script name
main.nf
Script ID
c2275107d1eafbc01b31ce8cf99ccbd7
Workflow session
21bcbfa1-8a99-4785-bd98-2b7987412e29
Workflow profile
test_full
Nextflow version
version 23.07.0-edge, build 5875 (28-07-2023 20:27 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

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(tasks table omitted because the dataset is too big)